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/*=========================================================================
*
* Copyright Insight Software Consortium
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
/**
*
* \author Ken Urish
*
* An example program to see how ThresholdMaximumConnectedComponentsImageFilter
* works for the Insight Journal:
*
* Urish KL, August J, Huard J. "Unsupervised segmentation for myofiber
* counting in immunoflourescent images". Insight Journal.
* ISC/NA-MIC/MICCAI Workshop on Open-Source Software (2005)
*
* Dspace handle: https://hdl.handle.net/1926/48 */
// itk header files
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkThresholdMaximumConnectedComponentsImageFilter.h"
int itkThresholdMaximumConnectedComponentsImageFilterTest( int argc,
char * argv [] )
{
if( argc < 3 )
{
std::cerr << "Usage: " << argv[0] << std::endl;
std::cerr << " 1: InputImage Name 2:OutputImage Name" << std::endl;
std::cerr << " 3: minimumPixelArea" << std::endl;
return EXIT_FAILURE;
}
typedef unsigned char InputPixelType;
typedef unsigned char OutputPixelType;
const unsigned int Dimension = 2;
typedef itk::Image< InputPixelType, Dimension > InputImageType;
typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
InputPixelType maxLabel = itk::NumericTraits<InputPixelType>::max();
InputPixelType minLabel =
itk::NumericTraits<InputPixelType>::NonpositiveMin();
const unsigned int minimumPixelArea = atoi( argv[3] );
typedef itk::ImageFileReader< InputImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( argv[1] );
// Read the Input Image
std::cout << "About to load input image " << std::endl;
try
{
reader->Update();
}
catch(itk::ExceptionObject & err)
{
std::cerr << "Exception Caught!" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
// ************************************************************************
// Automatic Threshold Filter
// This filter essentially chooses the optimum place to threshold the object.
// It also indirectly will count the number of objects for you.
// As a note, SetInsideValue(maxLabel)/SetOutsideValue(minLabel) will count
// the number of light objects. If the reverse, it will count the number of
// dark objects.
unsigned int numberOfObjects;
unsigned int thresholdValue;
typedef itk::ThresholdMaximumConnectedComponentsImageFilter< InputImageType>
ThresholdType;
ThresholdType::Pointer automaticThreshold = ThresholdType::New();
automaticThreshold->SetInput( reader->GetOutput() );
automaticThreshold->SetMinimumObjectSizeInPixels( minimumPixelArea );
// For counting Myofibers, the inside value should be the minLabel
// If you wanted to count a solid object (ie dapi nuclei) set the
// inside value to minLabel.
//
automaticThreshold->SetInsideValue( minLabel );
automaticThreshold->SetOutsideValue( maxLabel );
try
{
automaticThreshold->Update();
}
catch(itk::ExceptionObject & err)
{
std::cerr << "Exception Caught!" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
numberOfObjects = automaticThreshold->GetNumberOfObjects();
thresholdValue = automaticThreshold->GetThresholdValue();
std::cout << "Number of Objects = " << numberOfObjects << std::endl;
std::cout << "Threshold Value = " << thresholdValue << std::endl;
// *****************************************************************
// Image File Writer
typedef itk::ImageFileWriter< OutputImageType > WriterType;
WriterType::Pointer writer = WriterType::New( );
writer->SetInput( automaticThreshold->GetOutput() );
writer->SetFileName( argv[2] );
try
{
writer->Update();
}
catch(itk::ExceptionObject & err)
{
std::cerr << "Exception Caught!" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
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